


Mass Effect: Run and Hide

by ArcticLucie



Category: Mass Effect
Genre: Angst, Earthborn (Mass Effect), Fluff and Angst, M/M, Post-Refuse, Refuse Ending, Renegade Commander Shepard, multiple character deaths
Language: English
Status: Completed
Published: 2014-11-08
Updated: 2014-11-15
Packaged: 2018-02-24 14:21:38
Rating: Mature
Warnings: Graphic Depictions Of Violence, Major Character Death
Chapters: 3
Words: 5,777
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/2584475
Author URL: https://archiveofourown.org/users/ArcticLucie/pseuds/ArcticLucie
Summary: <blockquote class="userstuff">
              <p>Shepard refuses the Catalyst's choices and has to face the consequences. No matter how dire the situation seems, his only concern is keeping Kaidan and his crew alive. A tall order with the galaxy on the brink of extinction. Will he pull it off, or is his cycle destined to become another name on the Reapers' resume of death?</p><p>***I had originally intended to expand on this, but just closed it out because I lost interest among other things.***</p>
            </blockquote>





	1. Run

**Author's Note:**

> This is my first attempt at a post-refusal ending so hopfully it's not too off canon. The story starts mid conversation after the in-game dialogue.  
>  
> 
> Warning: Short, but somewhat graphic, Tali death scene.

"You are an illogical machine. You're broken, flawed. You're reasoning is fucked! I've proven you wrong, but you're too damn stubborn to accept it."

"I am doing what needs to be done to control the chaos," said the Catalyst.

"Bullshit! You're doing whatever the hell you want. I solved the organics versus synthetics conflict singlehandedly and I'm only Human! You are inferior! You should be taking orders from ME! I should be choosing YOUR fate."

"Then choose to control us!" demanded the white cluster of photons roughly formed into the outline of a small boy. It knew Shepard well, as did all the Reapers, and wisely took the form of the image that haunted his dreams night after night. 

"NO!" replied Shepard smugly, arms crossed over his chest in typical stubborn Shepard fashion. Pain be damned!

"Choose to take your rightful place atop your thrown!" It was beginning to anger, if machines were capable of such things.

"I'd rather die a thousand, million deaths than to join your army!" Shepard yelled back. "What would stop me from doing the same exact thing you were programmed to do, or programmed them to do, and leading the charge against the next cycle? Or would I control them like some kind of god? Will I be able to order them to lay down and be destroyed? Cause that's what I'd do! How about making them self-destruct? Then I'd be the only one left and they could worship me. Reaper Shepard has a nice ring to it, don't you think?

"But I'd never choose to be one of your homicidal machines!! And certainly not without proof and assurance that I could kill you all in the end, if I choose, leaving all the organic lifeforms in peace. Because I'm not willing to risk the possibility that I'd be unleashing the fury of a Reaperized me on everyone I've ever known."

"Then destroy us!" barked the AI.

"And destroy the good machines? The logical machines? The ones that are far superior than you'll ever be? The ones that have vowed to stand by my side? The ones who joined you because they had no choice? You're crazy! Now that they do have a choice, they choose me! And your army probably would too.

"I leave no man left behind! If I have to risk the possibility of billions of lives in my attempt to save them all, then I will! Because every SINGLE one of them is worth it! And I didn't have to indoctrinate my army to earn their loyalty."

"You're emotions cloud your judgement. Or is it your ego?" it asked.

"I guess that's one of the hazards of being Human, being an organic. Emotions. They're something you'll NEVER understand, and it's why we'll fight to the death against you," growled Shepard as his face began to burn due to his rage. "Although your ego clouds your's as well. But unlike me, you don't seem to notice."

"Your only other option is to join organics with synthetics. It's the only way you can save them all! The only way your cycle survives intact is through synthesis," said the hologram. It was beginning to throw a tantrum as its patients wore thin.

"I can't make that decision for a countless trillion species! I won't. Altering every living thing in the galaxy is something that no being should have the power to do, has the power to do! It's unnatural, ungodly, unfair to them all. And impossible. What kind of life would that be? What kind of monsters would be created? 

"What happens to the organisms who evolve afterward? What will stop them from creating synthetics for themselves? Or will it sterilize every possible inhabitable planet that hasn't yet established life? Or freeze every race in its technological tracks? What will keep any of them from building new machines? Newsflash, you won't, you can't. Although, none of this would be a problem if you'd use your powers for brokering peace instead of instigating war and destruction that you're so keen on.

"How is that even possible anyway? How would you, I mean, morphing living tissue into mechanical parts? Mechanical parts into flesh? Mixing them together? It's NOT possible! You're illogical AND full of shit!"

"SO BE IT!" screamed the high pitched voice as it disintegrated into nothingness.

"Come back here you little SHIT!" he yelled. "You coward! Just like the rest of the Reapers!" he spun around as the lights over the consuls dimmed. The panels began to move and a screeching sound emanated from where metal scratched against metal. 

"You've waited hundreds of cycles for someone to stand here where I'm standing and all you can manage is a five minute conversation? Five minutes to decide the fate of everyone in the galaxy? Five FUCKING minutes is all I get to negotiate? GET BACK HERE AND FACE ME!!!"

The weight of the galaxy was on his shoulders. He spent months getting resources for the war effort and the Crucible Project, years preparing for this day. And in an instant, it was all gone. Their hail Mary, their plan Z, their only hope for survival slipped through his hands before he knew what hit him.

If he had any sort of heart at all, he may have felt remorse. If he had a conscience, maybe regret. A fleeting thought of being responsible for the lives of the entire galaxy ran through his mind, but he shook it off. The Reapers were responsible. Their creator was the culprit. He/She/It set the whole thing in motion. The choices the Catalyst offered were unacceptable. 

Especially so, if he had to die to carry them out. He was okay with dying in battle, on the battlefield, but not at the hands of this Catalyst. He saw its flaws and refused to be a part of its ultimate plan. Not to mention, he had no way of knowing whether or not the entity was telling the truth.

It could have been an elaborate plot, indoctrination, an illusion. What if he was still on Earth hallucinating from his injuries? What if this was Hell? Or Purgatory? What if it was a trick to dispatch of the galaxy's only hope? All's fair in love and war, after all. And they were at war. What if it was a trick? He couldn't take that chance. 

Now, he and the entire galaxy would have to face the consequences of that decision. They would have to find another way or perish like the countless civilizations before them. He was given a choice to destroy, control, or synthesize the Reapers. He refused. He chose nothing, and in doing so, he may have condemned everyone in the galaxy to the same fate of the thousands of cycles before them. 

"Commander? Can you hear me? Answer me dammit!" bellowed Joker from the Normandy. They had lost his comms signal after the last time he talked to Admiral Hackett. 

"Joker, I need Tali or a Geth or someone who can hack. The Catalyst shut down. The Crucible won't fire!"

"I have you're position. They'll be there in five."

"They have three!" 

Four minutes later, Tali arrived on scene with backup. James managed to get them to an airlock close by with a kodiak they picked up from another ship after Cortez went down on Earth. Shepard pointed them to one of the terminals that had disappeared back into the floor. The engineer crew hurried over to see what they could do.

"James had to leave. He was a sitting duck out there," explained Tali as she rushed passed him. "Did I say that right?"

"We have to find a way to fire this thing! If we don't..."

"We know what's at stake," she said somberly. "You look pretty bad, Commander. I think you need to get back to the Normandy. You need medical attention. Where is your armor?"

"I think it was vaporized when I was hit by Harbinger. He definitely broke some ribs. Joker, how's it looking out there?" he asked through winces of pain.

"We got this, Commander. GO!" she ordered. 

He looked at her in protest before sucking in a deep breath. It stung as a rib bone dug into his lung. On further examination, he decided to do as she suggested. "Are you sure you'll be okay?"

"Of course. Especially with my two new Geth Prime bodyguards," she said smirking to herself in her mask.

"Vega, come get me," he said through the comms.

"That's a negative, Commander, another shuttle is on its way," Joker answered with a shaky voice.

"Where's James?" he asked with confusion. 

"We lost contact."

"Scans indicate that he was shot down by Reaper forces," said EDI with a monotoned voice. She was not successful in conveying the emotion of the moment.

"Where? Is he okay? Send someone to get him," ordered Shepard as he limped his way to the airlock Tali had used.

"He is gone, Shepard," EDI reiterated.

It was the second casualty sustained by the Normandy crew. He swallowed hard and hoped it would be the last. There was no time to blame himself; he had to get back to his ship. He managed to drag himself to the airlock where he waited for the shuttle.

"Shepard, I...," shrieked Tali with horror out of the silence. Her voice was like fingernails on a chalkboard. The shrill sound punctured his eardrums and scraped the inside of his skull.

"Tali? What's your status?"

"THE PRIMES!! THEY TURNED! Ahhh," her voice trailed off into nothing. She had managed to override the security system before the Geth were reprogramed by the Catalyst. It had hacked their Reaper codes, wiped their software, cut off communication with the Geth servers, and put them back under Reaper control.

Without warning, they turned on her. One ripped off her helmet and nearly took her head off with it. The other grabbed her shoulder and dislocated it. She struggled to break free, but they subdued her. The first pinned her other arm. She kicked the hard metal machines but it only sent pain shooting up her leg. The second gripped the base of her skull and gave a sharp twist. In an instant, she was dead.

"TALI?!" he yelled. She didn't answer.

"I'm sorry, Shepard. She is gone," replied EDI.

Three down and they were no closer to stopping the Reapers then they were four years ago. He resisted the urge to fall to his knees and weep. It would've been counterproductive. They would have wanted him to press onward and save the rest of their shipmates. 

A kodiak arrived a minute later. An unfamiliar pilot pulled him onto the shuttle and another punched it to the Normandy. He grimaced and grabbed his side as he slide down into the nearest chair. It was a shuttle from one of the medical ships but was commandeered by the Normandy after James went down. 

"GET ME HACKETT!" Shepard ordered.

"Patching him through," said Joker.

"FALL BACK!! It didn't work. WE HAVE TO FALL BACK! The Crucible failed," he admitted. As he spoke the words, an unimaginable fear came over him. It was surreal. He wished it was a dream. It felt like a dream. But the pain was unmistakable; he was awake.

"Repeat!" ordered Hackett in stunned disbelief.

"FALL BACK to rendezvous B! EARTH IS LOST!"

"No, that can't be right!" said the Admiral. He was in denial, as were everyone else within earshot of the conversation. Earth was going to be their last stand, and now they ended up falling flat on their asses.

"The Crucible, the Catalyst, they didn't work. We have no choice! EARTH IS DECIMATED. There's hardly anyone left down there....It's worse than Thessia." His voice crack as the images of all the fallen soldiers he saw in the last few years flashed through his mind.

"I...I, we..." Shepard was speechless. There were no words for an occasion like this. "I warned everyone. Why didn't you people listen? Now, Earth is being ripped apart. We have to retreat," he said more to himself than anyone else.

"Understood, Commander," said Hackett. "ALL FORCES FALL BACK TO RENDEZVOUS B! I REPEAT, RENDEZVOUS B!"

"But Admiral, what about Earth?" asked a man to the admiral's right. "We can't just..." Hackett looked at the man through sunken eyes. They were deadened by the weight of the words.

"EARTH IS LOST! FALL BACK!" he ordered. Their only hope now was to get as many people to the rendezvous before the Reapers noticed their retreat. 

"Were all the Geth hacked by the Catalyst, EDI?" Shepard asked.

"No, Shepard. No other units are showing any sign of Reaper control. It may have been their proximity to the Catalyst that sparked their malfunction."

"Admiral, get the Geth out of here. The Catalyst hacked a few units on the Citadel. We can't risk losing them," said Shepard as they began docking procedures with the Normandy.

"Understood, Commander. Hackett out," he said as he dropped the comms. 

"Joker, get us the hell out of here," he ordered as he nearly fell out of the kodiak onto the Normandy. Garrus and Doctor Chakwas were there to catch him as he stumbled onto the floor. He saw blurs of faces as they wheeled him up to the med-bay on a gurney.

"Don't put me under," he demanded after they transferred him to an operating table. 

"Commander, that would be unwise. I cannot risk you moving an inch while I have a laser poking around inside you," said the Doctor.

Garrus was staring down at him with hollow eyes. Liquid stained the Turian's face; his girlfriend was dead and guilt washed over him. Garrus had promised to keep her safe. He tried to go with her when Shepard called, but she refused to let him. For an instant, he blamed Shepard before pushing the thought out of his mind. 

"I need to be awake!" said Shepard.

"It'll only be for thirty minutes or so," she replied.

"I'll be right here," said Kaidan as he lightly squeezed his hand, brown eyes, warm and full of worry. How could he resist those eyes? Shepard finally nodded in approval before they shared a deep kiss. Shorty after, his lids grew heavy as he succumbed to their darkness.


	2. Hide

**Summary for the Chapter:**

> Shepard and Co. attempt to hide.

When he woke up, the lights where dim. He could feel Kaidan's warm body pressed against his side. Both of his hands were wrapped tightly around Shepard's arm as if he was clinging on for dear life, which he was.

He gave the Major the once-over. His shoulder was wrapped in thick bandages, and there were bruises all over his soft brown face. A cut intersected his eyebrow. Shepard grinned sweetly knowing that they'd both have the same scar. One finger was wrapped in a splint, and he had a cast on his ankle. He wished for nothing else but to remain in that moment forever, but he had a job to do.

"Joker, sitrep," he ordered. His voice woke Kaidan.

"We're a day out from the rendezvous. Everyone else seems to be keeping up. We lost a third of our ships. Reports from Earth are...not good."

"I could've told you that. Any messages?"

"No, everyone's running silent."

"Casualty report?" he asked hesitantly. That's not something he really wanted to hear; a rundown of all the people he lost, all the people he failed.

"Tali, Cortez, James, Jack, Jacob, Anderson, most of the Rachni, most of Humanity, Earth," he said with contempt. Shepard couldn't tell if it was directed at him or the Reapers. At that moment, he could not care less either way.

"Any good news?"

"What do you think? What the hell happened down there, Shepard?" he questioned. "The Crucible was supposed to work! We were supposed to destroy them! It's gone! Everything is GONE! Everything is FUCKED!"

"I don't know," is all he could say. His words were drenched in solemn emotion. He pinched the bridge of his nose and sighed deeply. "I don't know," he repeated.

He could feel Kaidan's warm breath on his skin. He wanted to disappear into his arms forever. He wanted to runaway with him to someplace else, anyplace else, to a different galaxy, a different universe. Kaidan placed a hand on his cheek for support and comfort while Shepard pulled him close and kissed his forehead. It burned with a slight fever from his wounds.

He still had Kaidan. That's all that mattered to him. If he lost Kaidan, he'd lose himself. Earth fell. Anderson was dead. Tali, Jack, Steve, James, Ash, Legion, Wrex; they were all gone. Billions of innocent lives sniffed out with ease. But keeping Kaidan alive was his only concern, his only focus.

He pushed him away, rose from the table, and turned until his legs dangled over the edge. A sharp dagger ripped through his lungs as he moved, and he thought about laying back down. His whole body was stiff, muscles aching, head pounding.

"Hey? Where are you going? You need to rest," said Kaidan with a firm voice.

"I need to get to the war room. We..."

"You're no good to us broken," interjected the Major.

"You wouldn't want me if I was broken? Thanks, K," he quipped. He turned to grab him by his thick black hair. The pain was excruciation but the kiss made it worth the trouble. "I didn't think so!" he snickered.

Kaidan laughed that soft laugh he used when Shepard caught him in a lie before admitting, "I'll take you any way I can, Love."

"Shepard, Hackett's on vidcom for you," Traynor interrupted.

"On my way," he said, slowly and carefully pulling on the shirt that was folded by the bed. He left the room without saying a word. Kaidan grabbed the crutches by his side and hobbled after him.

**XoXoX**

"We lost most of the Krogan in our retreat. Wreav...was among the casualties," relayed the Admiral. Shepard shook his head with frustration. His friends, his family, his allies, were falling left and right around him and he was powerless to stop it.

"Grunt made it to a Quarian ship. I'm sorry about Tali. She was a good egg."

"Thanks, Admiral." The words were meaningless.

"I'm afraid we also lost contact with Miranda. She had made her way onto the Citadel after you left. She was looking for a way to fire the damn thing. She's assumed M.I.A.."

"Any more 'good' new?" Shepard asked.

"We lost a third of our remaining fleet. I ordered all communications from Earth to cease. It...was too hard hearing all their cries for help. We, we've lost," he replied with stunned bewilderment.

"The Quarians lost a live ship. Some of the others refused to meet us at the rendezvous. A heavy assault has taken out communications with Sur'Kesh. Thessia went quiet days ago...It's only bad news," the admiral continued.

Shepard stood there hunched over the railing. His knuckles grayed as he gripped the metal to steady himself. During the last few weeks he saw planet after planet fall at the mercy of the Reapers. They fought back tooth and nail but it always, ALWAYS, ended in utter failure.

Every cycle before them had been through the same thing. Despair, destruction, dismemberment. Death. Their last hope was gone. Like the Protheans before them, they were going to lose. It was the first time that Shepard knew it to be true, the first time he admitted it to himself.

"Orders?" he asked the visibly shaken Hackett. The weight of the defeat was just as much his responsibility as Shepard's.

"I...I have none. Just try to stay alive. Try to keep your crew alive. Let's just make it to the rendezvous and go from there."

"Yes, sir."

"What?...No?!" he heard Hackett say over vidcom. "Shepard, Major Kirrahe just informed me that the entire Salarian Union went down along side the remaining Council fleet. They refused to follow us to the rendezvous. Instead, they made their way to Sur'Kesh."

"How's he holding up?"

"The comms went dark halfway through the transmission. His status is unknown."

"It just keeps getting better," he said as he felt his breathing increase. Suddenly, the room went dark.

**XoXoX**

He woke up back down in the infirmary two hours later. The bright lights pierced his pupils like a million hot needles. Kaidan was there holding his hand, sitting by the bed, head resting on the table. Shepard cleared his throat and the noise startled him as he looked up. His whiskey brown eyes met Shepard's fiery blues, and he did his best to force a smile.

"What happened?" Shepard asked.

"You're stubborn ass passed out," he lectured. "You died again, you coded twice! I told you NEVER to do that to me again!" It was worse than his fury on Horizon, on Mars.

"I..."

"You're sorry? Yeah...you say that a lot," Kaidan interrupted rolling his eyes. His words stung as did his grip on Shepard's arm, but there was no way he was going to let him go now.  
"But I am," he said, looking at him with surprise that faded to a sly grin.

"I know, but you're not leaving that table until I say you can," he ordered with a forcefulness that Shepard had yet to see before. He liked it. He wanted more of it in every way possible.

The only ounce of sympathy, of empathy, he ever had, he gave to Kaidan. The only thing he ever loved, the only person he ever gave a shit about was sitting next to him. Kaidan had torn through his armored soul like it was tissue paper and was nuzzled so far into his chest that they were now one being.

He was still the fucked up little boy orphaned on Earth years ago. He was only fighting the Reapers out of pride and his sense of duty, but he was trying to save the galaxy for Kaidan. To keep him safe, to protect him like he promised that he would. He had finally found his soul mate and nothing was ever going to separate them again.

"We're coming up to the relay, Commander," said Joker. "The Geth have finished with the upgrades and have hacked its transmission software. We are clear to proceed to the rendezvous."

"Where's Hackett?"

"He's an hour behind us. The rest of the fleet are an hour behind that. Do we proceed?"

"No. We go together. No need activating the relay any more than necessary."

"Aye, Commander."

**XoXoX**

An hour later, the doors to the med-bay opened. Admiral Hackett walked through. His disheveled appearance did little to convey the chaos raging inside of him. He had the vague outline of a plan scattered throughout his mind.

"Shepard, no need to sit up. We are way past formalities," he assured him. He sighed deeply upon seeing the broken body of the galaxy's hero. Where had they gone wrong?

"Are you sure this will work?" he asked the Commander.

"No, but at this point, it's our only option."

"That's what we said about the Crucible."

"And at the time, we were correct. This is our last chance. We have to go! I don't see any other way."

"What if they're waiting on the other side?" asked Kaidan. He hesitated before answering his own question. "They're on this side, too. I guess it won't make much of a difference."

"I'm staying," said the Admiral. It was followed by a long pause. "I'm going to ask for volunteers to stay and fight. I don't know how much of a difference it'll make, but I have to do it."

Shepard knew his decision was a death sentence. The Reapers indiscriminately killed every sentient being they'd ever come across while the lower species were left to evolve for the next cycle. However, he was not about to argue.

"We lost the whole damn line of Turian Primarchs, I think Garrus is next, and two Quarian admirals. Samara and most of the Asari, too."

"DAMMIT," yelled Shepard. "They're taking everyone from me! I'm staying! I can't let them get away with this!"

"No, you're going through. Someone needs to lead them. You're the face of this war. They'll follow you...That's an order."

"Why? I failed them."

"Don't be so hard on yourself," said Kaidan rubbing his forearm. They were way passed rules and regulations at this point.

"I'm heading to the CIC. As soon as the ships arrive, I'll make the announcement. You take everyone else through the relay," instructed Hackett.

"And then what?" asked Kaidan. A look of confusion colored his face.

"And then you try to survive," he said as he turned to leave. "No one will ever know you went through the relay. We can't risk the intel getting back to the Reapers."

**XoXoX**

Once the remaining ships under Hackett's command arrived, the announcement was made. He asked for help to rejoin the fight for Earth as the rest of the intergalactic fleet continued on to their destination.

Most of the Krogan volunteered to go with him. A few were transferred to a Salarian ship in exchange for a potential Genophage cure. Mordin had altered his appearance and accompanied them under an alias. Shepard convinced Grunt not to go with Hackett, instead he went with Mordin. He wanted someone he trusted to lead the Krogan if they made it back from the other side.

The last two remaining leaders of the Human Race said their "goodbyes". Hackett entered the airlock before setting out with the Sixth Fleet. Before the door closed, Shepard was given a battlefield promotion to Admiral of the remaining ships.

Less than four thousand Krogan, a little over six thousand each of Hanar, Drell and Batarians, sixteen thousand Geth, twenty thousand Salarians, thirty thousand Turians, thirty-four thousand Asari, forty-four thousand Quarians, and sixty-two thousand Humans were under his control. It wasn't much, but it would have to do.

"Joker, we're going through first. We'll send a signal back if it's clear," said Shepard as he sat in the co-pilot's seat. Kaidan had helped him from the med-bay. He knew there was no way in hell, he'd be able to keep him confined to the infirmary.

"What if this doesn't work?" asked an unsure Kaidan.

"Then we die," Shepard replied with an emotionless expression. Kaidan squeezed his shoulder in a show of solidarity. Garrus stood behind them. The next time Shepard died, they were determined to go with him.

"Another suicide run? Why the fuck not?" said Joker as he hit the throttle.

The red glow from the Omega relay poured through the windows. Three of the four held their breath as they accelerated towards the galactic core. It had been less than a year since the trio, minus Kaidan, did the same thing when they defeated the Collectors. What would they find on the other side? Reapers? Collectors? Sanctuary? Certain death?

Shepard knew the Illusive Man had gone through it at least once since then to retrieve the Human Reaper. Right out of the relay, the debris field they encountered the first time around had dissipated some. He thought the Illusive Man probably had something to do with that.

"Okay, send the message, Joker," he ordered after they scouted the area. It was in an old Earth communication code so as not to call attention to themselves.

"Aye, aye, Commander."

Ships appeared out of thin air from the other side of the relay. In the past few hours, the ships were outfitted with a copy of a modified Reaper IFF software compliments of the Geth. If all else failed, as it had, they were to be an ark for the next cycle. Before going through, the captains were instructed to go against everything they were ever taught; they were told to run and hide.

Roll call was taken after every ship had arrived. A scheduled rotation was put into place for their contact with the Normandy. All nonessential communication was stopped. They were to float aimlessly camouflaged within the debris field until the Reapers retreated into the dark space.

Twenty minutes later, Dr. Chakwas made her way to the cockpit. She wanted to retrieve her two most difficult patients. Garrus had a hold of Shepard and Dr. Chakwas helped the Major as they turned to walk down the bridge corridor.

Out of nowhere, the ship shook and an alarm sounded while green lights flickered over head. In a split second, Shepard was pushed into the cockpit escape pod by Garrus who landed on top of him with a thud, heavy armor pressing into his ribs. He looked to his left and caught Kaidan's eye who was pushed in by Dr. Chakwas.

"WHAT THE FUCK WAS THAT?!" screamed Shepard as they were jettisoned into space.

"A piece of debris hit the drive core. It flooded the entire ship with radiation. Everyone on board is dead," EDI's voice answered over the comms system.

  
"WHAT THE FUCK? How is that possible? We had our shields up! Why wasn't Joker notified so he could take evasive action? WHY DIDN'T YOU DO IT?! This sure as shit better not be one of your pranks!"

"It is not, and we did not. Harbinger clipped us, as Joker said, and knocked out quite a few of our systems. We tried our best to repair them all, but life support was more important than shields at the time," EDI explained. "I am sorry, Shepard."

"Why wasn't I informed? WHY? Wh..." He tried unsuccessfully to swallow the lump that had formed in his throat.

Tears began to pour down Kaidan's face at the news. He buried his face in Shepard's tender chest and began to sob. Shepard showed no emotion. He was pretty much dead inside already. The only thing he felt was throbbing creeping through his body and Kaidan's warm hand on his. Maybe a hint of rage.

"LIARA?" yelled Garrus. "ANSWER ME!" he demanded.

"She is gone, Garrus," replied EDI. "Everyone is gone. Traynor, Adams...Joker."

"WHAT? That can't be right! We were just onboard and everyone was fine. Just take us back."

"Garrus, there are no life signs on board the Normandy. Everyone is dead. The ship needs to be vented of radiation before you can return."

"No...no, that can't be right. We lost our homes; we were not supposed to lose our friends! We're supposed to be safe here, Shepard!" demanded Garrus as he tried his best to console Dr. Chakwas who was near hysteria.

"We aren't safe anywhere, Garrus," Shepard replied. "I'm sorry...it's, it's all my fault...i should've..."

His conversation with the Catalyst raced through his mind. He pulled Kaidan as close and as tight as he could. Pain be damned! He may have doomed the entire galaxy to death, but somehow he still had Kaidan. And for him, maybe that was enough, maybe that would forever be enough.

"No, it's the Reapers' fault!" Kaidan managed to say as Shepard tried to wipe away his tears. "What do we do now?" he asked, his brown eyes pleading for guidance and comfort, Garrus' beady ones doing the same.

"We follow Hackett's order...we try to stay alive."

**Notes for the Chapter:**

> I hope this was not too OC or unbelievable with the Omega Relay. And that killing off the rest of the crew didn't seem too forced. I had a goal to kill off as many people as I could. Joker deserved to die on his ship, but Shepard still needed it.


	3. Prologue

**Summary for the Chapter:**

> Ugh, decided to give up on this one. Just reposting the prologue I had up before.

After the Normandy's meltdown, Geth were dispatched to make repairs. The ship was up and running within a week. It would be Shepard's home for the rest of his life. The bodies of his crew were buried with honors. They received a full military funeral before they were hurled towards the galactic core. Their names were added to the memorial wall on the crew deck along with everyone else they had lost.

Life beyond the Omega relay was rather dull. There was nowhere to travel to, little to no entertainment, and nothing to shoot at. Shepard's days were spent with boring administrative tasks; the nights were spent in Kaidan's arms. He made the days bearable and the nights worth living.

They found ways to use the Quarian fleet's innovations to feed the masses and insure their survival. After a few years, more ships were constructed out of the remains of others in the debris field. In the beginning, they had a population decline, but as soon as they worked out the kinks, expansion was a necessity. 

The Geth were invaluable to everyone, doing heavy repairs, aiding with software and hardware upgrades and installations, rigging up a new Geth Consensus. Everyone was hesitant at first, but they were incredible allies. It only strengthen Shepard's resolve that he made the right choice. The Catalyst was wrong!

Surprisingly, not many interspecies conflicts arose. They established a new Council with Shepard at the top, and every ship and species had a representative. Everyone understood their importance. They would have about fifty thousand years to prepare for the next invasion after the Reapers left the galaxy, it they were lucky. Everyone thought they'd need every second of it after the disaster they had witnessed over the past few months.

They had one close call with a Reaper about ten years after they arrived. One came through the relay to inspect the area. Fortunately, Geth patrols were able to get the fleet a message before it hit the relay. Every ship went silent and the Reaper passed by without noticing them.

The Geth had managed to make upgrades to their software to prevent anymore Reaper hacks. They were also able to use bits of the Reaper codes and technology they salvaged in the debris to better camouflage themselves and the fleet. 

A hundred years later, Shepard took his last breath. He was laying in his bed aboard the Normandy intertwined with Kaidan; their bodies melding into one like they had a million nights before. They died within fifteen minutes of each other peacefully in their sleep. It was as if the universe could not bare to separate them, even in death. 

Two hundred years later, the fleet population surpassed half a million. The Krogan Genophage was updated. They had fewer children at a time, but they were healthy and most survived. The Quarians, thanks to the Geth, were finally free of their suits. Grunt was the first Krogan Ambassador.

Three hundred years later, they began increasing patrols through the relay. They journeyed further and further out searching for signs of Reapers. After three hundred and twelve years, the big machines had disappeared into the void from whence they came. When news reached the Council, a fleet wide announcement went out. Every species, every ship, every individual, heard it simultaneously. 

It simply said: Activate the Shepard Protocol.

**Notes for the Chapter:**

> I really wanted to highlight the contributions of the Geth here. Take that Starbrat!! I also think this would make an incredible story, watching the civilizations rebuild and how they'd pass on their importance to their children and the desperation to prepare for the next cycle. It could have been a brilliant way to set up a new trilogy. But I digress. Hope you liked it!

**Author's Note:**

> The second half to follow next week.
> 
> P.S. I really hate the catalyst, if it wasn't obvious by Shepard laying into it. Hope it wasn't too over-the-top and that their conversation made sense.


End file.
